Table 2 |
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|
Validation of microarray gene expression data |
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|
Symbol |
Assay ID |
Tumors |
Metastases |
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|
|
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|
CtR |
CtS |
Ratio |
p value |
CtR |
CtS |
Ratio |
p value |
||
|
|
|||||||||
|
Fully validated genes |
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|
CHEK1* |
CHEK1-Hs00176236_m1 |
30.3 |
30.9 |
2.2 |
2.11E-02 |
29.8 |
31.9 |
4.0 |
2.87E-03 |
|
CHEK2* |
CHEK2-Hs00200485_m1 |
29.3 |
30.1 |
2.5 |
3.40E-04 |
29.0 |
30.9 |
2.0 |
8.33E-03 |
|
COL4A2 |
COL4A2-Hs00300500_m1 |
25.2 |
23.5 |
-3.7 |
1.60E-06 |
24.9 |
23.5 |
-4.3 |
5.27E-07 |
|
COL6A1 |
COL6A1-Hs00242448_m1 |
24.8 |
21.9 |
-6.6 |
3.45E-08 |
25.9 |
24.6 |
-2.0 |
9.54E-03 |
|
COL6A2 |
COL6A2-Hs00365167_m1 |
24.8 |
21.6 |
-8.6 |
8.66E-08 |
25.1 |
24.0 |
-2.8 |
5.40E-05 |
|
FOS |
FOS-Hs00170630_m1 |
21.5 |
21.1 |
-2.7 |
2.36E-03 |
22.1 |
21.6 |
-3.0 |
2.86E-06 |
|
HRASLS3 |
HRASLS3-Hs00272992_m1 |
27.6 |
25.2 |
-5.6 |
3.42E-07 |
25.7 |
25.7 |
-2.4 |
2.14E-05 |
|
LAMB1 |
LAMB1-Hs00158620_m1 |
24.6 |
23.4 |
-2.4 |
5.25E-04 |
25.3 |
24.1 |
-2.8 |
8.46E-06 |
|
MMP11 |
MMP11-Hs00171829_m1 |
25.4 |
23.6 |
-3.1 |
1.85E-05 |
25.6 |
23.0 |
-10.2 |
2.46E-08 |
|
PEA15 |
PEA15-Hs00269428_m1 |
24.4 |
23.5 |
-2.4 |
4.52E-04 |
24.5 |
23.7 |
-2.3 |
2.50E-05 |
|
RAD51 |
RAD51-Hs00153418_m1 |
26.6 |
27.7 |
2.3 |
9.81E-03 |
26.2 |
28.0 |
3.0 |
4.23E-03 |
|
RECQL4* |
RECQL4-Hs00171627_m1 |
27.6 |
28.3 |
2.1 |
1.26E-03 |
27.0 |
29.0 |
3.7 |
2.41E-03 |
|
RERG |
RERG-Hs00262869_m1 |
31.8 |
28.5 |
-11.1 |
5.07E-12 |
31.2 |
30.5 |
-3.4 |
2.10E-06 |
|
RRAGD |
RRAGD-Hs00222001_m1 |
29.6 |
27.0 |
-7.8 |
1.74E-07 |
28.5 |
26.9 |
-3.0 |
2.60E-05 |
|
SERPINF1 |
SERPINF1-Hs00171467_m1 |
26.1 |
23.7 |
-3.5 |
2.52E-05 |
24.6 |
24.7 |
n/a |
n/a |
|
TGFBI |
TGFBI-Hs00165908_m1 |
23.9 |
22.0 |
-5.4 |
2.35E-06 |
24.0 |
21.6 |
-6.7 |
7.27E-08 |
|
TP53 |
TP53-Hs00153340_m1 |
24.0 |
25.2 |
2.5 |
7.00E-03 |
24.0 |
25.4 |
2.9 |
3.21E-03 |
|
BCL2 |
BCL2-Hs00608023_m1 |
29.7 |
29.5 |
n/a |
n/a |
29.2 |
29.5 |
1.1 |
6.86E-01 |
|
E2F4 |
E2F4-Hs00608098_m1 |
23.0 |
22.6 |
-1.1 |
8.34E-01 |
22.8 |
23.2 |
-1.3 |
1.94E-01 |
|
ITGB6 |
ITGB6-Hs00168458_m1 |
27.5 |
27.8 |
-1.0 |
9.16E-01 |
26.9 |
27.7 |
-1.0 |
9.32E-01 |
|
RAD52 |
RAD52-Hs00172536_m1 |
29.4 |
28.5 |
-1.9 |
1.12E-02 |
28.5 |
28.6 |
-1.1 |
5.42E-01 |
|
TOP1 |
TOP1-Hs00243257_m1 |
25.1 |
24.8 |
-1.1 |
7.89E-01 |
24.6 |
26.2 |
1.1 |
8.14E-01 |
|
Validated genes |
|||||||||
|
CASP1 |
CASP1-Hs00354832_m1 |
26.6 |
27.6 |
2.1 |
5.91E-03 |
28.6 |
28.3 |
-1.5 |
1.80E-01 |
|
MAD2L1 |
MAD2L1-Hs00829154_g1 |
26.7 |
27.5 |
2.0 |
9.91E-03 |
27.0 |
27.7 |
1.4 |
2.72E-01 |
|
False discoveries |
|||||||||
|
ABCA2 |
ABCA2-Hs00242232_m1 |
26.2 |
26.0 |
1.0 |
9.94E-01 |
25.9 |
26.0 |
-1.1 |
6.59E-01 |
|
ABL1* |
ABL1-Hs00245445_m1 |
26.2 |
25.7 |
-1.3 |
3.05E-01 |
26.2 |
26.1 |
-1.3 |
2.91E-01 |
|
TOP2B |
TOP2B-Hs00172259_m1 |
25.4 |
25.1 |
-1.2 |
3.19E-01 |
25.1 |
25.6 |
-1.1 |
5.46E-01 |
|
CES2 |
CES2-Hs00187279_m1 |
26.2 |
24.6 |
-2.8 |
5.41E-04 |
24.2 |
24.6 |
2.0 |
2.33E-02 |
|
JUN |
JUN-Hs00277190_s1 |
22.8 |
22.1 |
-1.6 |
1.86E-02 |
22.1 |
22.3 |
-2.5 |
9.00E-06 |
|
TGFB1 |
TGFB1-Hs00171257_m1 |
25.8 |
23.8 |
-3.5 |
2.70E-06 |
24.8 |
24.5 |
-2.2 |
5.83E-05 |
|
|
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|
Q-PCR validation step on a series of 30 genes. For each gene, symbol and TaqMan® assay (assay ID) are indicated; asterisks refer to TaqMan® single assays. Genes displayed in bold were considered for further Q-PCR analysis of new samples from additional patients (compare Figure 3 and Additional data file 7); italics refer to genes selected as not significantly differentially expressed with microarrays. The threshold cycle CtS refer to chemo-sensitive states and CtR to resistant states; the expression changes (ratio) are specified as negative (down-regulated) or positive (up-regulated) values between resistant versus sensitive samples. Adjusted p values were computed using z statistics with false discovery rate corrections (α = 0.05). n/a, not analyzed. |
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|
Graudens et al. Genome Biology 2006 7:R19 doi:10.1186/gb-2006-7-3-r19 |
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